R Graphics with ggplot2
ggmap and the Google Maps Static API
Evan Muzzall
November 4, 2019
Package installation
install.packages("ggmap")
library(ggplot2)
library(cowplot)
library(dplyr)
library(ggmap)Challenge
1. Create six graphs
Load the the ggplot2 cheatsheet and the iris dataset to create six visualizations and combine them into a single figure.
Note the code for custom colors.
data(iris)library(ggplot2)
iris_density = ggplot(iris, aes(x = Petal.Length, fill = Species)) +
geom_density(alpha = 0.5) +
theme_bw() +
theme(legend.position = "bottom") +
scale_fill_manual(values = c("orange", "yellow", "cyan"))
iris_density
iris_scatter = ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width,
color = Petal.Length)) +
geom_point(size = 4, alpha = 0.5) +
theme_bw() +
theme(legend.position = "left") +
scale_color_gradient(low = "red", high = "blue")
iris_scatter
iris_box = ggplot(iris, aes(x = Species, y = Sepal.Length,
fill = Species)) +
geom_boxplot() +
theme_bw() +
guides(fill = FALSE) +
scale_fill_manual(values = c("goldenrod", "salmon", "turquoise"))
iris_box
iris_bar = ggplot(iris, aes(x = Sepal.Width)) +
geom_bar(stat = "count",
color = "black",
fill = "blue") +
theme_bw()
iris_bar
iris_jitter = ggplot(iris, aes(x = Petal.Length, y = Sepal.Length,
color = Species)) +
geom_jitter(size = 4, alpha = 0.5,
height = 3, width = 3) +
theme_bw() +
theme(legend.position = "top") +
scale_color_brewer(palette = "Blues")
iris_jitter
iris_smooth = ggplot(iris, aes(x = Petal.Length, y = Petal.Width,
color = Species)) +
geom_point(size = 4, alpha = 0.5) +
geom_smooth(color = "red", lwd = 1, se = FALSE) +
theme_bw() +
theme(legend.position = "right") +
scale_color_hue(l = 40, c = 35)
iris_smooth## `geom_smooth()` using method = 'loess' and formula 'y ~ x'
library(cowplot)##
## ********************************************************## Note: As of version 1.0.0, cowplot does not change the## default ggplot2 theme anymore. To recover the previous## behavior, execute:
## theme_set(theme_cowplot())## ********************************************************iris_compound = plot_grid(iris_scatter, iris_jitter, iris_smooth,
iris_box, iris_density, iris_bar)## `geom_smooth()` using method = 'loess' and formula 'y ~ x'iris_compound
ggsave(filename = "visuals/iris_compound.pdf", plot = iris_compound,
width = 12, height = 8, units = "in", dpi = 600)2. Maps!
The data
For this mapping example, we will use the first 1000 rows from the Obervation.org nature dataset from the Netherlands housed at the Global Biodiversity Information Facility (GBIF) (login required; citation, citation guidelines, data user agreement.
gbif = read.csv("data/gbif_1000.csv", stringsAsFactors = TRUE,
sep = "\t")
head(gbif)## gbifID datasetKey
## 1 1951966751 8a863029-f435-446a-821e-275f4f641165
## 2 1951966752 8a863029-f435-446a-821e-275f4f641165
## 3 1951966753 8a863029-f435-446a-821e-275f4f641165
## 4 1951966754 8a863029-f435-446a-821e-275f4f641165
## 5 1951966755 8a863029-f435-446a-821e-275f4f641165
## 6 1951966756 8a863029-f435-446a-821e-275f4f641165
## occurrenceID kingdom phylum class
## 1 https://observation.org/observation/89083645 Animalia Arthropoda Insecta
## 2 https://observation.org/observation/89083599 Animalia Chordata Aves
## 3 https://observation.org/observation/89083416 Animalia Chordata Aves
## 4 https://observation.org/observation/89083564 Animalia Chordata Aves
## 5 https://observation.org/observation/89083635 Animalia Chordata Aves
## 6 https://observation.org/observation/89083429 Animalia Chordata Aves
## order family genus species
## 1 Lepidoptera Nymphalidae Aglais Aglais io
## 2 Passeriformes Corvidae Coloeus Coloeus monedula
## 3 Accipitriformes Accipitridae Circus Circus macrourus
## 4 Passeriformes Turdidae Turdus Turdus merula
## 5 Passeriformes Fringillidae Chloris Chloris chloris
## 6 Charadriiformes Alcidae Uria Uria aalge
## infraspecificEpithet taxonRank scientificName
## 1 SPECIES Aglais io (Linnaeus, 1758)
## 2 SPECIES Coloeus monedula (Linnaeus, 1758)
## 3 SPECIES Circus macrourus (S.G.Gmelin, 1770)
## 4 SPECIES Turdus merula Linnaeus, 1758
## 5 SPECIES Chloris chloris (Linnaeus, 1758)
## 6 SPECIES Uria aalge (Pontoppidan, 1763)
## verbatimScientificName verbatimScientificNameAuthorship countryCode
## 1 Aglais io NA NL
## 2 Coloeus monedula NA NL
## 3 Circus macrourus NA NL
## 4 Turdus merula NA NL
## 5 Chloris chloris NA NL
## 6 Uria aalge NA NL
## locality stateProvince occurrenceStatus
## 1 Veenendaal Utrecht NA
## 2 Colijnsplaat - Haven Zeeland NA
## 3 Texel - Eierland - Oorsprongweg - west Noord-Holland NA
## 4 Koudekerke Zeeland NA
## 5 Vlieland - Waterzuivering Friesland NA
## 6 IJmuiden - Zuidpier Noord-Holland NA
## individualCount publishingOrgKey decimalLatitude
## 1 1 c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f 52.00
## 2 6 c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f 51.60
## 3 1 c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f 53.10
## 4 1 c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f 51.45
## 5 1 c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f 53.25
## 6 1 c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f 52.45
## decimalLongitude coordinateUncertaintyInMeters coordinatePrecision
## 1 5.55 5000 NA
## 2 3.85 5000 NA
## 3 4.80 5000 NA
## 4 3.55 5000 NA
## 5 5.05 5000 NA
## 6 4.50 5000 NA
## elevation elevationAccuracy depth depthAccuracy eventDate day
## 1 NA NA NA NA 2014-10-10T00:00:00Z 10
## 2 NA NA NA NA 2014-10-10T00:00:00Z 10
## 3 NA NA NA NA 2014-10-10T00:00:00Z 10
## 4 NA NA NA NA 2014-10-10T00:00:00Z 10
## 5 NA NA NA NA 2014-10-10T00:00:00Z 10
## 6 NA NA NA NA 2014-10-10T00:00:00Z 10
## month year taxonKey speciesKey basisOfRecord institutionCode
## 1 10 2014 4535827 4535827 HUMAN_OBSERVATION NA
## 2 10 2014 6100954 6100954 HUMAN_OBSERVATION NA
## 3 10 2014 2480491 2480491 HUMAN_OBSERVATION NA
## 4 10 2014 2490719 2490719 HUMAN_OBSERVATION NA
## 5 10 2014 5845582 5845582 HUMAN_OBSERVATION NA
## 6 10 2014 2481342 2481342 HUMAN_OBSERVATION NA
## collectionCode catalogNumber recordNumber identifiedBy dateIdentified
## 1 Observations OBS.89083645 NA NA NA
## 2 Observations OBS.89083599 NA NA NA
## 3 Observations OBS.89083416 NA NA NA
## 4 Observations OBS.89083564 NA NA NA
## 5 Observations OBS.89083635 NA NA NA
## 6 Observations OBS.89083429 NA NA NA
## license rightsHolder recordedBy typeStatus
## 1 CC_BY_NC_4_0 Stichting Natuurinformatie NA NA
## 2 CC_BY_NC_4_0 Stichting Natuurinformatie NA NA
## 3 CC_BY_NC_4_0 Stichting Natuurinformatie NA NA
## 4 CC_BY_NC_4_0 Stichting Natuurinformatie NA NA
## 5 CC_BY_NC_4_0 Stichting Natuurinformatie NA NA
## 6 CC_BY_NC_4_0 Stichting Natuurinformatie NA NA
## establishmentMeans lastInterpreted mediaType issue
## 1 NA 2019-09-20T15:16:10.208Z NA
## 2 NA 2019-09-20T18:27:13.067Z NA
## 3 NA 2019-09-20T18:04:30.994Z NA
## 4 NA 2019-09-21T02:02:55.492Z NA
## 5 NA 2019-09-20T18:08:17.611Z NA
## 6 NA 2019-09-21T00:22:32.721Z NAConnecting to the Google Maps Static API
If you want to add your data to Google Maps, you must first 1) enable the Maps Static API and 2) enable billing by entering your credit card information. Don’t worry though, Google gives you a bunch of free credits and will not charge you without your permission.
Click “Go to console”
Login with a gmail account and click “Create Project” and enter your information
Click the hamburger and then “APIs and Services”
Click “+ Enable APIs and Services” and search for “Maps Static API”, then click “Enable”
Click the hamburger and then “APIs and Services”
Click “Credentials” then “Create Credentials” then “API key”
You should see a popup window that says “API key created” - click “Restrict key”, then select “Restrict key”, click the dropdown menu and select “Static Maps API” and then save
In the searchbar, type “billing” and select “Billing”, click “Manage Billing Accounts” and then “Add Billing Account”. Enter your information and select “Save and enable billing”
Copy your API key into the below code:
## Google's Terms of Service: https://cloud.google.com/maps-platform/terms/.## Please cite ggmap if you use it! See citation("ggmap") for details.##
## Attaching package: 'ggmap'## The following object is masked from 'package:cowplot':
##
## theme_nothingggmap::register_google(key = "YOUR API KEY HERE") # choose the lat/lon from the first row in the gbif dataset as the center point
# you might want to find something more central!
netherlands = ggmap(get_googlemap(center = c(lon = 5.55, lat = 52.00),
zoom = 7, scale = 2,
maptype = "terrain",
color = "color"))## Source : https://maps.googleapis.com/maps/api/staticmap?center=52,5.55&zoom=7&size=640x640&scale=2&maptype=terrain&key=xxxnetherlands
ggsave(filename = "visuals/netherlands.pdf", plot = netherlands,
width = 12, height = 8, units = "in", dpi = 600)If this does not work, you might need the GitHub version of ggmap
devtools::install_github("dkahle/ggmap")
library(ggmap)Now, we can plot the rest of the data on the Google Map
gbif_center_point = c(lon = 5.55, lat = 52.00)
gbif_map = get_map(gbif_center_point, zoom = 7) ## Source : https://maps.googleapis.com/maps/api/staticmap?center=52,5.55&zoom=7&size=640x640&scale=2&maptype=terrain&language=en-EN&key=xxx# Country overlay
netherlands_data = ggmap(gbif_map) +
geom_point(data = gbif, alpha = 0.5,
aes(x = decimalLongitude, y = decimalLatitude,
col = kingdom))
netherlands_data
ggsave(filename = "visuals/netherlands_data.pdf", plot = netherlands_data,
width = 12, height = 8, units = "in", dpi = 600)
# Facet by province
netherlands_facet = ggmap(gbif_map) +
geom_point(data = gbif, alpha = 0.5,
aes(x = decimalLongitude, y = decimalLatitude,
col = kingdom)) +
ggtitle("Observation variation by Netherlands province") +
facet_wrap(~stateProvince)
netherlands_facet
ggsave(filename = "visuals/netherlands_facet.pdf", plot = netherlands_facet,
width = 12, height = 8, units = "in", dpi = 600)Be sure to click “Shut Down” on your Google Cloud project when you are done so that it does not run in perpetuity :)